MCC – Metal Complexation Calculation

MCC – Metal Complexation Calculation
software for
calculation of metal complexation parameters from experimental titration data, and
simulation of metal complexation titrations
Instructions for use
Dario Omanović
Ruđer Bošković Institute
Center for Marine and Environmental Research
Laboratory for Physical Chemistry of Traces
Zagreb, Croatia
[email protected]
May, 2014.
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DISCLAIMER
MCC – Metal Complexation Calculation is software for the calculation of complexation parameters (ligand
concentrations and conditional stability constants) by fitting of experimental titration data. This software
is Windows-based and is currently not supported by Mac OS.
MCC is available free of charge, and the author is not responsible for any negative consequences which
could arise from its use. As such, users are advised to use the software entirely at their own “risk”.
At current, stage licensing is not needed to use MCC, but in future version(s) users will be invited to
provide some basic information to author (kind of free registration).
This software is updated regularly and users are advised to obtain the latest version by manual or autoupdate (under development). The latest version of MCC can be downloaded at:
http://gss.srce.hr/pithos/rest/[email protected]/files/Software/
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Table of contents
Page
1. Data Fitting Procedure
4
1.1. Insertion of titration data into MCC Data Table
4
1.2. Data Fitting Steps (“Calculations” Tab)
5
2. Graphical Interface
11
3. Numerical Data Tab
13
4. Opening/Saving MCC Data Files and Software Update
14
5. Simulation of Titration Curve
15
Appendix I. Registration of “fitter.dll” file
16
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INTRODUCTORY NOTE
In order to fit the titration data, MCC needs the fitter.dll file. MCC will try automatically to unpack and register
the file, however on more recent versions of windows (usually 64-bit platforms), a manual registration is needed.
Appendix I contains instructions for manual “fitter.dll” registration.
1.0 DATA FITTING PROCEDURE
1.1 INSERTION OF TITRATION DATA INTO MCC DATA TABLE
The easiest way to insert titration data into the MCC is to follow these steps (Figure 1):
1. prepare two columns for titration data (total metal and signal intensities) in Excel (or similar
program, see below)
2. select the range of titration data you want to treat
3. copy data into Clipboard (CTRL+C)
4. open the MCC software
5. select “Data Table” tab
6. right click on the first box on the table and choose “Paste Data” to paste the copied data into the
table or simply press CTRL+V on your keyboard
Figure 1 Two column set of selected titration data prepared in Excel (left figure), same data in
MCC after insertion (right figure).
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The first column should contain the total metal concentrations and the second column, the corresponding
signal intensities. Upon insertion, in the third column (“Use”), number one (1) will be assigned for each
titration point, which means that the point(s) will be used in the data treatment. To discard a particular
data point (e.g. outlier) double click on the selected row and zero (0) will be assigned, and the titration
point will be omitted from the calculation. Simply double-click again to reassign value to one (1) to reinclude the discarded point(s).
For proper calculation of complexation parameters, total metal concentrations in the first column should
be expressed in Molar concentrations. If for example in the excel table concentrations are written in
nMols, use “1e-9” as
in MCC to convert them in Molar values. In example
below, concentrations in excel are written in Molar values, so factor one (1) is assigned to “Paste X
factor”. The same apply for the signal intensities.
By default, table with data is “locked”, however if user wants to change some values, check the
box.
Other than Excel, data can be prepared in any text editor, such that the data are in two columns, X and
Y, and separated by “Space” or “Tab” as shown below
1.00E-09
1.36E-09
1.85E-09
5.42E-11
8.88E-11
1.33E-10
…
Note: In some cases copying and pasting data from Excel will not take into account all decimal places,
so users are advised to be vigilant of the number of decimal places are inserted into MCC. For the
example above, data in the Excel table are formatted to two decimal places; however, copying and
pasting to MCC, resulted in additional decimal places due to the “Paste Format” (this was correct way
of data transfer). At least three significant numbers are recommended.
Once data are inputed, switch to the “Calculations” tab.
1.2 DATA FITTING STEPS (“CALCULATIONS” TAB)
Follow these steps in order to properly apply data fitting routine:
1.
2.
3.
4.
define sensitivity/slope
if applicable, define side reaction coefficients (inorganic and Added Ligand, AL)
select model on which data will be fitted (one, two or three ligand classes)
chose and press desired “fitting method”
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Step 1: Slope/sensitivity
By default, when data are inserted/pasted into the “Data Table”, the last five (5) data points of the
titration curve are used for the first approximation of the sensitivity/slope (S) (Figure 2, marked area).
Figure 2 Initial setup of sensitivity/slope
Number of points used for slope approximation could be changed by using corresponding
control.
NOTE: The slope assigned using last titration points is not theoretically correct because the titration curve
is only asymptotically approaching real (non-complexing) slope. In the case of “very” strong ligand(s),
the defined slope is a good approximation, however in case of relatively “weak” ligand(s), its use could
lead to incorrect complexation parameters and it is NOT recommended.
The
control on the right side of the Slope value could be used for slope adjustment. The relative
adjustment step is controlled by the Step percentage (1% or 0.1%). If necessary, user may manually insert
a predefined value for the slope. Once inserted, press ENTER to assign the new slope, which will be
update/ in the graphs on the right panel.
NOTE:
option is still under development/testing and therefore it is not recommended to
use it for slope adjustment.
Step 2: Side reaction coefficients
In order to express conditional stability constants based on free metal concentration (e.g. Cu2+, Fe3+,…),
both inorganic and added ligand, “AL” side reaction coefficients must be defined (Figure 3).
Figure 3 Setup of side reaction coefficients
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NOTE: The recommended option is for users to make their own “database” of “Added Ligands” and their
corresponding stability constants. To do that, open
the top main toolbar.
window (Figure 4) by pressing button on
Figure 4 Metal Side Reaction Coefficients (SRC) window (database)
“Metal Side Reaction Coefficients (SRC)” table allows setup of up to three stability constants for metalAL complexes and one (1) corresponding inorganic SRC. In order to create new “Item”, press “Add new”.
New row in the table will be added. In first column insert “ID” (name) for the new “Item” (see examples
on Figure 4). In second column, define number of metal-added ligand (MAL) species, i.e. stability
constants which will be inserted (usually two). In above example, for Inorganic Cu it is zero, whereas for
Cu-SA it is two (2). Last column is reserved for inorganic side reaction coefficient of metal. (Usually, MAL
stability constants are defined according to salinity, and consequently, corresponding inorganic side
reaction coefficient should be used).
Note that MAL side reaction coefficients should be expressed as logarithmic values, whereas Inorganic
SRC as decade value.
Once necessary fields in table are filled, press “Save” to store database on the disk. By default, data are
stored in the same folder as MCC program (file: “SRC_Data.txt”).
To remove “Item” from the database, click on the desired row and click
click
. Subsequently,
in order to update changes in database file.
allows user to insert only concentration of added ligand (AL), and the program will calculate
corresponding side reaction coefficient for MAL.
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NOTE: After inserting concentration of AL, press ENTER to apply changes, otherwise it possible that
the new SRC will be not assigned.
Apart from the “database”, the Inorganic SRC and MAL SRC values could be manually inserted into the
corresponding boxes.
Step 3: Selection of the model and setup of initial complexation parameters (“Initial guess”)
Once the slope and SRCs are defined, user should select the model on which data will be fitted. Models
with one, two and three ligand classes are available for selection (Figure 5).
Figure 5 Setup of model and initial parameters for Non-linear fitting
Before initiating the fitting, initial values for complexation parameters should be defined. User can either
manually enter the ligand concentrations and stability constants, or simply press
button,
and program will automatically assign initial values. By default, first five (5) and last five (5) titration points
will be used for estimation of initial complexation parameters for L1 and L2 ligand, respectively.
NOTE: If error/warning window appears in “initial guess” estimation process, increase the number of
titration points.
Automatically calculated initial complexation parameters could be further adjusted by using
control.
Based on the entered complexation parameters, a titration curve will be calculated and plotted as BLUE
LINE on all four graphs. Any changes in the complexation parameters will cause immediate recalculation
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and modification of the curves on all graphs. If the curve is not automatically plotted or updated, click
button to refresh the graphs.
Note: After the fitting is performed, calculated complexation parameters will be presented in this section.
Click
if you want to copy complexation parameters to “Simulation” section (this
option is used only for testing purposes).
Step 4: Calculation of complexation parameters – Non-linear Fitting
After the above steps are completed, the user should decide which “fitting model” will be used. In case
“one-ligand” model is selected, four (4) different options are available, while for two or more ligand
model, three (3) options are available (Figure 6):
1.
- relationship total metal concentrations (Mt) vs. measured/found
concentrations (Mf) will be fitted (this is opposite to titration curve where measured/found
concentrations are in function of total metal)
2.
– relationship of “ML” vs “Mfound” (measured Me) will be fitted
(“Langmuir/Gerringa model”)
3.
4.
– classical “Ružić-van den Berg model”
– in case of one ligand model, data could be fitted on the second order
polynomial roots equation (“Lorenzo model”).
Figure 6 Commands/options for fitting
For all these four options, user can select
and/or
. In weighted fit,
2
weights defined as 1/Y will be assigned to each Y-value, whereas for enhanced fit, all XY data will be
transformed in logarithmic values.
“Enhanced fit” is selected by default, but there is no recommendation which “combination” to use for
fitting. It is left to the user’s “discretion” to select the model of fit.
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NOTE: An error messages (e.g. Catastrophic failure!) could appear during process of fitting. Two main
reasons leading to these errors are (i) inadequate initial fitting parameters or (ii) impossibility to perform
fitting using defined ligand model and fitting method. In first case, user should only adapt initial
parameters (“Initial Guess”) and restart the fitting. The second case usually appears if inadequate ligand
model and/or fitting method is selected (e.g. fitting “one-ligand titration data” on two or three ligand
model). If there is no satisfactory “combination”, in most cases the problem is due to the inadequate
(bad) raw titration data, meaning that experiment should be repeated.
User is also advised to check titration points for outliers.
“Recommended” titration point number depends on their “quality”, however at least 10-15 points are
ideal, assuming that titration is performed in adequate concentration range.
Once fitting is accomplished, the calculated complexation parameters are displayed in fields within “NonLinear Fitting” box and the “blue” curve is overlayed on experimental points on all graphs.
Uncertainties of each parameter are computed by the fitting algorithm (fitter.dll) in the MCC and are
expressed as 95% Confidence Intervals.
If user wants to perform and compare different “combinations” of fitting models, it is advisable to make
a list of the calculated complexation parameters by clicking the
to add results to
existing list (Figure 7). Fitted parameter results could be copied and transferred in other program for
further analysis.
Figure 7 “Non-linear Fitting Results” window
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2.0 GRAPHICAL INTERFACE
Experimental points and fitted curve are presented using four different graphs (Figure 8a and 8b):
1. Titration graph (Mf vs. Mt)
2. Langmuir/Gerringa transformation (ML vs. Mf)
3. Ružić-van den Berg transformation (Mf/ML vs. Mf)
4. Scatchard transformation (ML/Mf vs. ML)
(Mf – metal found, i.e. measured conc.; Mt – total metal conc.; ML – conc. of formed metal complex with natural ligand).
Figure 8a Transformation graphs plotted in linear scale
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Figure 8b Transformation graphs plotted in logarithmic scale
Default tab presents four graphs on one page (“All Plots” tab), but user can select each graph separately
for larger viewing using other Tabs. Besides these four graphs, the “original” titration curve is presented
on first tab
NOTE: By pressing CTRL+L combination on the keyboard, the axes on all graphs will switch between
linear or logarithmic scales. By right mouse click, a pop-up menu with option “Copy plot to Clipboard”
will appear allowing selected plot to be copied and transferred in other application.
Error distribution graph representing percentage difference between experimental and fitted values can
be displayed by pressing
button on the top main toolbar (Figure 9). A value of average
absolute error is provided within the window. If the proper model is selected, it is expected that positive
and negative errors are “randomly” distributed along the titration curve. Any curvature trend/shape
suggests an inadequate ligand-model selection.
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Figure 9 Error distribution graph
3.0 NUMERICAL DATA TAB
The
tab (Figure 10) contains four tables: in the leftmost one, experimental points and
three transformations are listed, in the middle one corresponding fitted “points” are listed (blue curve)
and the right one is used to list inorganic and free metal concentrations based on the calculated (fitted)
complexation parameters. The rightmost table is the free input field, where user can write some notes.
User can use right click and “Copy Selected” or Ctrl+C or simply click
button above the
tables to copy whole table. Part of the selected cells could be copied by right click and “Copy selected”.
By default, the first value of total metal concentration from titration curve (assumed to represent
ambient total metal concentration in sample) is used for calculation of free metal concentration. User
can manually add more total metal concentrations for which inorganic and free concentrations will be
calculated by pressing
could be used for this calculation.
button.
or
(default) complexation parameters
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Figure 10 Numerical Data tab
4.0 OPENING/SAVING MCC DATA FILES AND SOFTWARE UPDATE
After performing fitting or simulation, users are advised to save the titration data and fitted parameters
(Figure 11). Press “Save MCC Data” button on top toolbar (or Menu command, File>Save data) and save
file under selected file name and location. Use “Load MCC data” to open saved file(s).
By pressing Menu command Check for Update (within Misc), a pop-up window will appear informing the
user of the location where new version of MCC can be downloaded. Note: Before downloading the
updated version, the opened (running) version should be closed, otherwise it will be not updated.
Figure 11 “Load/Save MCC Data” buttons on top toolbar; Check for Update option
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5.0 SIMULATION OF TITRATION CURVE
An option to simulate titration experiment is available in MCC (Figure 12), however its use will be
described in updated version of this manual.
Figure 12 Simulation Tab
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Appendix I. Registration of “fitter.dll” file
By default, if the fitter.dll is not present in the folder where MCC is located, MCC will automatically extract the file
and save it.
32bit windows
Copy „fitter.dll“ to windows system32 directory (e.g. C:\Windows\System32\fitter.dll)
Open RUN window (or Command Prompt if RUN command is not available in start menu):
Insert command: regsvr32 fitter.dll and press OK (the same is if using Command Prompt)
If all is OK, the following window will appear and MCC.EXE will function without I/O error.
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64bit windows
You should be registered as administrator for proper registration.
1. delete fitter.dll from system32 directory (if exist)
2. copy fitter.dll in ..\WINDOWS\SYSWOW64\ directory
3. run "regsvr32 fitter.dll"
Contact author ([email protected]) if the problems in registering “fitter.dll” persist.

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